Package list barrnap / 0cf501a
add patch to use nonfree HMMs if given Sascha Steinbiss 6 years ago
4 changed file(s) with 139 addition(s) and 1 deletion(s). Raw diff Collapse all Expand all
1010 Package: barrnap
1111 Architecture: all
1212 Section: science
13 Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
13 Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends},
14 libfile-temp-perl, hmmer (>= 3.1)
15 Suggests: barrnap-silva-hmms
1416 Description: rapid ribosomal RNA prediction
1517 Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
1618 ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea
00 use_debian_dirs
1 use_both_hmmsets
0 --- a/bin/barrnap
1 +++ b/bin/barrnap
2 @@ -4,8 +4,9 @@
3 use Time::Piece;
4 use List::Util qw(max);
5 use FindBin;
6 +use File::Temp qw/ tempfile tempdir /;
7
8 -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9 +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10 # global variables
11
12 my $EXE = $FindBin::RealScript;
13 @@ -29,13 +30,13 @@
14 );
15 my $MAXLEN = int( 1.2 * max(values %LENG) );
16
17 -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18 +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
19 # command line options
20
21 my(@Options, $quiet, $kingdom, $threads, $evalue, $lencutoff, $reject, $incseq);
22 setOptions();
23
24 -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25 +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
26 # check all is well
27
28 msg("This is $EXE $VERSION");
29 @@ -64,23 +65,38 @@
30 my $hmmdb = "$DBDIR/$kdom.hmm";
31 err("Can't find database: $hmmdb") unless -r $hmmdb;
32 msg("Using database: $hmmdb");
33 +my $nonfreehmmdb = "$DBDIR/nonfree/$kdom.hmm";
34
35 -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
36 +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
37 # run the external command
38
39 my $fasta = shift @ARGV;
40 $fasta && -r $fasta or err("Usage: $EXE <file.fasta>");
41
42 +if (-e $nonfreehmmdb) {
43 + # prepare full pHMM file (with nonfree if it exists)
44 + open ( HMMDB, "<", $hmmdb ) or die "Could not open file $hmmdb: $!";
45 + open ( NONFREE, "<", $nonfreehmmdb );
46 + my ($tmpfile, $tmpfilename) = tempfile();
47 + while ( my $line = <HMMDB> ) {
48 + print $tmpfile $line;
49 + }
50 + while ( my $line = <NONFREE> ) {
51 + print $tmpfile $line;
52 + }
53 + $hmmdb = $tmpfilename
54 +}
55 +
56 msg("Scanning $fasta for $kdom rRNA genes... please wait");
57 my $cmd = "$NHMMER --cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout \Q$hmmdb\E \Q$fasta\E";
58 msg("Command: $cmd");
59 my @hits = qx($cmd 2>&1);
60
61 -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
62 +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
63 # process the output
64
65 my @feat;
66 -HIT:
67 +HIT:
68 foreach (@hits) {
69 chomp;
70 err("nhmmer failed to run - $_") if m/fail|error|core dump|bus error/i;
71 @@ -102,7 +118,7 @@
72 # check for incomplete alignments
73 my $note = '';
74 my $len = $end-$begin+1;
75 -
76 +
77 if ( $len < int($reject * $LENG{$gene}) ) {
78 msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
79 next HIT;
80 @@ -120,7 +136,7 @@
81 ];
82 }
83
84 -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
85 +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
86 # output a sorted GFF3
87
88 sub gff_sort {
89 @@ -168,13 +184,13 @@
90
91 sub show_citation {
92 print STDERR << "EOCITE";
93 -
94 +
95 If you use Barrnap in your work, please cite:
96
97 Seemann T (2013)
98 $EXE $VERSION : $DESC
99 $URL
100 -
101 +
102 Thank you.
103
104 EOCITE
105 @@ -193,7 +209,7 @@
106 {OPT=>"help", VAR=>\&usage, DESC=>"This help"},
107 {OPT=>"version", VAR=>\&version, DESC=>"Print version and exit"},
108 {OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing $EXE"},
109 - {OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'bac',
110 + {OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'bac',
111 DESC=>"Kingdom: ".join(' ', values %KINGDOM) },
112 {OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
113 {OPT=>"threads=i", VAR=>\$threads, DEFAULT=>8, DESC=>"Number of threads/cores/CPUs to use"},
114 @@ -226,15 +242,15 @@
115 my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
116 $def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/;
117 my $opt = $_->{OPT};
118 - $opt =~ s/!$//;
119 - $opt =~ s/=s$/ [X]/;
120 + $opt =~ s/!$//;
121 + $opt =~ s/=s$/ [X]/;
122 $opt =~ s/=i$/ [N]/;
123 $opt =~ s/=f$/ [n.n]/;
124 printf STDERR " --%-15s %s%s\n", $opt, $_->{DESC}, $def;
125 }
126 else {
127 print STDERR "$_\n";
128 - }
129 + }
130 }
131 exit(1);
132 }
0 use_debian_dirs
1 use_both_hmmsets